drake_md_report


HYPOTHESES

We selected only peaks seen in >1 of the 4 replicates (i.e. n = 2 or 3 or 4)


setup

how many FTICR reps per treatment type?

click to open
SampleAssignment reps
50-drought-groundw-control-Intact 2
50-drought-precip-C-Intact 2
1.5-drought-groundw-C-Homogenized 3
1.5-drought-groundw-C-Intact 3
1.5-drought-groundw-control-Homogenized 3
1.5-drought-groundw-N-Intact 3
1.5-drought-precip-C-Homogenized 3
1.5-drought-precip-N-Homogenized 3
1.5-fm-precip-C-Intact 3
1.5-fm-precip-N-Homogenized 3
50-drought-groundw-control-Homogenized 3
50-drought-groundw-N-Intact 3
50-drought-precip-control-Homogenized 3
50-fm-groundw-control-Intact 3
50-fm-groundw-N-Homogenized 3
50-fm-precip-control-Homogenized 3
50-fm-precip-N-Homogenized 3
1.5-drought-groundw-control-Intact 4
1.5-drought-groundw-N-Homogenized 4
1.5-drought-precip-C-Intact 4
1.5-drought-precip-control-Homogenized 4
1.5-drought-precip-control-Intact 4
1.5-drought-precip-N-Intact 4
1.5-fm-groundw-C-Homogenized 4
1.5-fm-groundw-C-Intact 4
1.5-fm-groundw-control-Homogenized 4
1.5-fm-groundw-control-Intact 4
1.5-fm-groundw-N-Homogenized 4
1.5-fm-groundw-N-Intact 4
1.5-fm-precip-C-Homogenized 4
1.5-fm-precip-control-Homogenized 4
1.5-fm-precip-control-Intact 4
1.5-fm-precip-N-Intact 4
50-drought-groundw-C-Homogenized 4
50-drought-groundw-C-Intact 4
50-drought-groundw-N-Homogenized 4
50-drought-precip-C-Homogenized 4
50-drought-precip-control-Intact 4
50-drought-precip-N-Homogenized 4
50-drought-precip-N-Intact 4
50-fm-groundw-C-Homogenized 4
50-fm-groundw-C-Intact 4
50-fm-groundw-control-Homogenized 4
50-fm-groundw-N-Intact 4
50-fm-precip-C-Homogenized 4
50-fm-precip-C-Intact 4
50-fm-precip-control-Intact 4
50-fm-precip-N-Intact 4

so we select formulae seen in at least 2 reps per treatment type


van krevelens

domains, baseline

fticr domains

VK by replication

VK by replication

VK by treatment

VK diagrams by treatment

VK unique

VK unique

unique to each amendment, in each incubation type


peaks

graphs

total peaks

complex:simple compounds

peak count tables

tables – total peaks

Homogenization Moisture Wetting 1.5-control 1.5-C 1.5-N 50-control 50-C 50-N
Intact drought groundw 736 ± 180 1598 ± 180 913 ± 381 884 ± 0 2155 ± 663 802 ± 70
Intact drought precip 1008 ± 274 1857 ± 208 1326 ± 49 1768 ± 194 2823 ± 0 1567 ± 129
Intact fm groundw 915 ± 124 698 ± 34 848 ± 196 1144 ± 273 1064 ± 137 1036 ± 201
Intact fm precip 596 ± 89 637 ± 61 497 ± 80 1181 ± 276 3149 ± 272 1423 ± 47
Homogenized drought groundw 2411 ± 136 1863 ± 245 1394 ± 221 2149 ± 205 3294 ± 290 992 ± 227
Homogenized drought precip 1121 ± 391 1089 ± 109 1227 ± 151 1261 ± 173 1576 ± 701 1829 ± 584
Homogenized fm groundw 933 ± 134 899 ± 176 490 ± 47 2475 ± 455 1408 ± 175 568 ± 119
Homogenized fm precip 1475 ± 209 609 ± 162 804 ± 129 2208 ± 141 3689 ± 339 844 ± 255

tables – complex peaks

Homogenization Moisture Wetting 1.5-control 1.5-C 1.5-N 50-control 50-C 50-N
Intact drought groundw 520 ± 143 1159 ± 181 583 ± 241 778 ± 0 1609 ± 507 594 ± 61
Intact drought precip 733 ± 204 1220 ± 136 977 ± 25 1469 ± 158 2109 ± 0 1148 ± 87
Intact fm groundw 590 ± 93 431 ± 16 442 ± 81 894 ± 233 689 ± 79 747 ± 166
Intact fm precip 374 ± 64 439 ± 51 345 ± 62 905 ± 207 2341 ± 175 1039 ± 43
Homogenized drought groundw 2175 ± 121 1535 ± 227 1030 ± 187 1767 ± 215 2818 ± 233 774 ± 204
Homogenized drought precip 889 ± 317 825 ± 90 978 ± 133 1045 ± 162 1396 ± 667 1488 ± 506
Homogenized fm groundw 677 ± 94 557 ± 120 331 ± 32 2094 ± 453 1065 ± 178 425 ± 79
Homogenized fm precip 1007 ± 100 379 ± 107 557 ± 106 1605 ± 95 3229 ± 285 687 ± 229

relative abundances

relative abundance of complex peaks

STATS

PERMANOVA

PERMANOVA

overall

#> 
#> Call:
#> adonis(formula = relabund_wide %>% select(aliphatic:condensed_arom) ~      (Amendments + Moisture + Wetting + Suction + Homogenization)^3,      data = relabund_wide) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                                     Df SumsOfSqs MeanSqs F.Model      R2
#> Amendments                           2   0.14437 0.07219   7.811 0.04766
#> Moisture                             1   0.21505 0.21505  23.270 0.07099
#> Wetting                              1   0.00916 0.00916   0.991 0.00302
#> Suction                              1   0.38447 0.38447  41.602 0.12691
#> Homogenization                       1   0.17475 0.17475  18.909 0.05768
#> Amendments:Moisture                  2   0.04268 0.02134   2.309 0.01409
#> Amendments:Wetting                   2   0.05754 0.02877   3.113 0.01899
#> Amendments:Suction                   2   0.02715 0.01357   1.469 0.00896
#> Amendments:Homogenization            2   0.13898 0.06949   7.519 0.04588
#> Moisture:Wetting                     1   0.01834 0.01834   1.985 0.00606
#> Moisture:Suction                     1   0.05683 0.05683   6.149 0.01876
#> Moisture:Homogenization              1   0.00560 0.00560   0.606 0.00185
#> Wetting:Suction                      1   0.04302 0.04302   4.655 0.01420
#> Wetting:Homogenization               1   0.05849 0.05849   6.329 0.01931
#> Suction:Homogenization               1   0.02368 0.02368   2.562 0.00782
#> Amendments:Moisture:Wetting          2   0.08926 0.04463   4.829 0.02946
#> Amendments:Moisture:Suction          2   0.03187 0.01593   1.724 0.01052
#> Amendments:Moisture:Homogenization   2   0.04422 0.02211   2.392 0.01460
#> Amendments:Wetting:Suction           2   0.03512 0.01756   1.900 0.01159
#> Amendments:Wetting:Homogenization    2   0.02055 0.01027   1.112 0.00678
#> Amendments:Suction:Homogenization    2   0.08361 0.04181   4.524 0.02760
#> Moisture:Wetting:Suction             1   0.02044 0.02044   2.212 0.00675
#> Moisture:Wetting:Homogenization      1   0.00995 0.00995   1.077 0.00328
#> Moisture:Suction:Homogenization      1   0.02605 0.02605   2.819 0.00860
#> Wetting:Suction:Homogenization       1   0.01140 0.01140   1.233 0.00376
#> Residuals                          136   1.25687 0.00924         0.41488
#> Total                              172   3.02945                 1.00000
#>                                    Pr(>F)    
#> Amendments                          0.001 ***
#> Moisture                            0.001 ***
#> Wetting                             0.368    
#> Suction                             0.001 ***
#> Homogenization                      0.001 ***
#> Amendments:Moisture                 0.052 .  
#> Amendments:Wetting                  0.017 *  
#> Amendments:Suction                  0.191    
#> Amendments:Homogenization           0.001 ***
#> Moisture:Wetting                    0.159    
#> Moisture:Suction                    0.004 ** 
#> Moisture:Homogenization             0.586    
#> Wetting:Suction                     0.015 *  
#> Wetting:Homogenization              0.005 ** 
#> Suction:Homogenization              0.073 .  
#> Amendments:Moisture:Wetting         0.001 ***
#> Amendments:Moisture:Suction         0.145    
#> Amendments:Moisture:Homogenization  0.058 .  
#> Amendments:Wetting:Suction          0.096 .  
#> Amendments:Wetting:Homogenization   0.347    
#> Amendments:Suction:Homogenization   0.004 ** 
#> Moisture:Wetting:Suction            0.124    
#> Moisture:Wetting:Homogenization     0.329    
#> Moisture:Suction:Homogenization     0.079 .  
#> Wetting:Suction:Homogenization      0.294    
#> Residuals                                    
#> Total                                        
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PERMANOVA for treatments

1.5 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_1_5 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = intact_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.00603 0.003014  0.4995 0.01288  0.754    
#> Moisture                     1   0.07530 0.075298 12.4784 0.16088  0.001 ***
#> Wetting                      1   0.05498 0.054976  9.1107 0.11746  0.001 ***
#> Amendments:Moisture          2   0.02583 0.012913  2.1399 0.05518  0.079 .  
#> Amendments:Wetting           2   0.04222 0.021109  3.4981 0.09020  0.017 *  
#> Moisture:Wetting             1   0.01142 0.011423  1.8931 0.02441  0.136    
#> Amendments:Moisture:Wetting  2   0.05315 0.026576  4.4042 0.11356  0.006 ** 
#> Residuals                   33   0.19913 0.006034         0.42545           
#> Total                       44   0.46805                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa intact cores

#> 
#> Call:
#> adonis(formula = intact_50 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = intact_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.08850 0.044252  5.8702 0.19694  0.001 ***
#> Moisture                     1   0.01117 0.011168  1.4815 0.02485  0.237    
#> Wetting                      1   0.01314 0.013136  1.7426 0.02923  0.181    
#> Amendments:Moisture          2   0.03599 0.017997  2.3875 0.08010  0.058 .  
#> Amendments:Wetting           2   0.02278 0.011392  1.5112 0.05070  0.222    
#> Moisture:Wetting             1   0.02859 0.028587  3.7923 0.06361  0.029 *  
#> Amendments:Moisture:Wetting  2   0.02308 0.011538  1.5305 0.05135  0.225    
#> Residuals                   30   0.22615 0.007538         0.50323           
#> Total                       41   0.44940                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

1.5 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_1_5 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = homo_1_5) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.11805 0.059026  7.9299 0.16791  0.001 ***
#> Moisture                     1   0.20467 0.204672 27.4967 0.29111  0.001 ***
#> Wetting                      1   0.01808 0.018077  2.4286 0.02571  0.078 .  
#> Amendments:Moisture          2   0.02850 0.014249  1.9143 0.04053  0.112    
#> Amendments:Wetting           2   0.03984 0.019918  2.6758 0.05666  0.046 *  
#> Moisture:Wetting             1   0.01283 0.012831  1.7238 0.01825  0.164    
#> Amendments:Moisture:Wetting  2   0.05037 0.025186  3.3836 0.07164  0.021 *  
#> Residuals                   31   0.23075 0.007443         0.32819           
#> Total                       42   0.70308                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

50 kPa homogenized cores

#> 
#> Call:
#> adonis(formula = homo_50 %>% select(aliphatic:condensed_arom) ~      Amendments * Moisture * Wetting, data = homo_50) 
#> 
#> Permutation: free
#> Number of permutations: 999
#> 
#> Terms added sequentially (first to last)
#> 
#>                             Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)    
#> Amendments                   2   0.19013 0.095065  6.7194 0.22768  0.001 ***
#> Moisture                     1   0.00599 0.005993  0.4236 0.00718  0.670    
#> Wetting                      1   0.03243 0.032430  2.2922 0.03884  0.128    
#> Amendments:Moisture          2   0.07244 0.036221  2.5602 0.08675  0.047 *  
#> Amendments:Wetting           2   0.03066 0.015328  1.0835 0.03671  0.401    
#> Moisture:Wetting             1   0.00933 0.009327  0.6593 0.01117  0.534    
#> Amendments:Moisture:Wetting  2   0.05551 0.027754  1.9617 0.06647  0.099 .  
#> Residuals                   31   0.43858 0.014148         0.52520           
#> Total                       42   0.83506                  1.00000           
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

PCA

overall PCA

PCA individual treatments

individual cores


others

other plots

NOSC

elements

Session Info

click to expand

Date run: 2020-08-17

#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Catalina 10.15.6
#> 
#> Matrix products: default
#> BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] lme4_1.1-23      Matrix_1.2-18    car_3.0-9        carData_3.0-4   
#>  [5] visNetwork_2.0.9 vegan_2.5-6      lattice_0.20-41  permute_0.9-5   
#>  [9] rmarkdown_2.3    drake_7.12.4     ggbiplot_0.55    PNWColors_0.1.0 
#> [13] forcats_0.5.0    stringr_1.4.0    dplyr_1.0.1      purrr_0.3.4     
#> [17] readr_1.3.1      tidyr_1.1.1      tibble_3.0.3     ggplot2_3.3.2   
#> [21] tidyverse_1.3.0  here_0.1        
#> 
#> loaded via a namespace (and not attached):
#>  [1] minqa_1.2.4        colorspace_1.4-1   ellipsis_0.3.1    
#>  [4] rio_0.5.16         rprojroot_1.3-2    fs_1.5.0          
#>  [7] rstudioapi_0.11    farver_2.0.3       soilpalettes_0.1.0
#> [10] fansi_0.4.1        lubridate_1.7.9    xml2_1.3.2        
#> [13] splines_4.0.2      knitr_1.29         jsonlite_1.7.0    
#> [16] nloptr_1.2.2.2     packrat_0.5.0      broom_0.7.0       
#> [19] cluster_2.1.0      dbplyr_1.4.4       shiny_1.5.0       
#> [22] compiler_4.0.2     httr_1.4.2         backports_1.1.8   
#> [25] assertthat_0.2.1   fastmap_1.0.1      cli_2.0.2         
#> [28] later_1.1.0.1      htmltools_0.5.0    prettyunits_1.1.1 
#> [31] tools_4.0.2        igraph_1.2.5       gtable_0.3.0      
#> [34] agricolae_1.3-3    glue_1.4.1         tinytex_0.25      
#> [37] Rcpp_1.0.5         cellranger_1.1.0   vctrs_0.3.2       
#> [40] nlme_3.1-148       xfun_0.16          openxlsx_4.1.5    
#> [43] rvest_0.3.6        mime_0.9           miniUI_0.1.1.1    
#> [46] lifecycle_0.2.0    statmod_1.4.34     MASS_7.3-51.6     
#> [49] scales_1.1.1       hms_0.5.3          promises_1.1.1    
#> [52] parallel_4.0.2     yaml_2.2.1         curl_4.3          
#> [55] labelled_2.5.0     stringi_1.4.6      highr_0.8         
#> [58] klaR_0.6-15        AlgDesign_1.2.0    filelock_1.0.2    
#> [61] boot_1.3-25        zip_2.1.0          storr_1.2.1       
#> [64] rlang_0.4.7        pkgconfig_2.0.3    evaluate_0.14     
#> [67] labeling_0.3       htmlwidgets_1.5.1  tidyselect_1.1.0  
#> [70] plyr_1.8.6         magrittr_1.5       R6_2.4.1          
#> [73] generics_0.0.2     base64url_1.4      combinat_0.0-8    
#> [76] txtq_0.2.3         DBI_1.1.0          pillar_1.4.6      
#> [79] haven_2.3.1        foreign_0.8-80     withr_2.2.0       
#> [82] mgcv_1.8-31        abind_1.4-5        modelr_0.1.8      
#> [85] crayon_1.3.4       questionr_0.7.1    progress_1.2.2    
#> [88] grid_4.0.2         readxl_1.3.1       data.table_1.13.0 
#> [91] blob_1.2.1         reprex_0.3.0       digest_0.6.25     
#> [94] xtable_1.8-4       httpuv_1.5.4       munsell_0.5.0